Renaming of search parameter sets

[Fredrik Levander]

It should be possible to rename search parameter sets. Also, the headings MascotParameterSets? and MascotParameterStorage? should get better titles.

[olle]

Ticket accepted.

[olle]

Design discussion.

Currently, Proteios SE differs in the click actions for the name column of different groups of item list tables:

• Many item lists in Proteios SE have a click action for the name column coupled to an action showing the properties for that item, where name, description, and possibly other properties might be edited and saved.
• Lists of search items, however, have the click action for the name column coupled to an action for viewing/editing the search parameters themselves, as this is most often what is desired.

Since the current click actions for the name column in lists of search items are appropriate, the following design is proposed for viewing/editing properties for search items:

• Each search item list table will be extended with a new tool bar button, "Properties".
• Clicking on the "Properties" button will forward to an action where you can view the properties of a search item selected in the item list by checking its check box. An error message should be displayed if no search item was selected, or more than one were selected.
• The search item properties form should have a "Save" tool bar button. Clicking on the "Save" button should forward to an action saving the new values of editable properties.
• At least the name and description should be editable. The XML file storing the search parameters and the search type for Mascot and OMSSA searches should be shown, but not be editable.
• Since the search item list tables are implicitly created by class ConfigureTableFactory2, they cannot be directly extended with a new tool bar button. This will therefore be performed by the search item properties class implementing an appropriate context, whereby a button coupled to the action automatically will be added to the table tool bar.

[olle]

(In [3989]) Refs #707. Refs #287. Refs #290. First version of support for editing of Mascot parameter set storage properties:

1. New class/file action/mascot/ViewMascotParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing MascotParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VMASCOTPARAMETERSETSTORAGEID in new class ViewActiveMascotParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/mascot/ViewActiveMascotParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VMASCOTPARAMETERSETSTORAGEID, and gets the corresponding MascotParameterSetStorage item, whose properties are shown using new form MascotParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveMascotParameterSetStorageProperties.

3. New class/file gui/form/MascotParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of a MascotParameterSetStorage item.

4. New class/file action/mascot/SaveMascotParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the MascotParameterSetStoragePropertiesForm form and saves them in the corresponding MascotParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

6. Default icon settings file "default" in icons/ in client/servlet/

updated with new icon assignments.

[olle]

Traceability note:

• Starting X!Tandem searches from Proteios was introduced in Ticket #362 (Run X! Tandem from Proteios).
• Starting OMSSA searches from Proteios was introduced in Ticket #471 (Searching OMSSA from Proteios SE).
• Starting Mascot searches from Proteios SE was introduced in Ticket #534 (Mascot GUI), and was updated in Ticket #623 (Multiple selections results in one job) and Ticket #710 (Select multiple databases for Mascot search).

[olle]

Note on names for search setting classes.

In order to clearly identify what variables are handled by a class used for search settings managed by Proteios SE, the intention was that the class name should reflect this, even if the name became rather long. Two main groups of classes exist for search settings, where the class name is based on the longest root string of one of the following (string _SEARCH_MACHINE_ should be exchanged for one of "Mascot", "OMSSA", or "XTandem"):

• _SEARCH_MACHINE_ParameterSet - The actual search settings (variables and values), normally 20 or more in number.
• _SEARCH_MACHINE_ParameterSetStorage - A full set of search settings, together with properties for the set as a single entity. Each set has a name, description, and an associated XML file containing the values of the search settings (parameters). In addition to the latter properties, special properties for some search machines might be included.

The idea of storing search settings in an XML file came from X!Tandem, where input data to a locally installed X!Tandem program (not working through a web interface), was supplied by an XML file of the same structure as used in Proteios SE. The intention was that users having such a locally installed X!Tandem program should be able to edit their settings in Proteios SE, and then either run the program from inside Proteios SE (not yet supported), or export the XML file for use externally with the search program. When parameter sets for OMSSA and Mascot searches were added, it was natural to also store these settings in XML files.

While there are reasons to keep the naming structure of the search settings classes, the names displayed in the GUI for search setting forms and tables may be changed to ones that are most informative for the user. This can be done using the normal localization method, see Ticket #287 (Labels and headers should display the correct English localization).

[olle]

(In [3992]) Refs #707. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new and updated string keys for Mascot parameter sets, in order to get better consistency with form for other search parameter sets.

[olle]

(In [3993]) Refs #707. Refs #362. Class/file action/xTandemInput/ListXTandemParameterSetStorage.java in client/servlet/ updated:

1. Public method void runMe() updated in table title key string,

in order to get better consistency with form for other search parameter sets.

[olle]

(In [3996]) Refs #707. Refs #534. Class/file gui/form/MascotParameterSetStoragePropertiesForm.java in client/servlet/ updated:

1.Public constructor MascotParameterSetStoragePropertiesForm() updated by change of table field set title key string to "MascotParameterSetStorageProperties?`", which is more appropriate.

[olle]

Subversion commit message to change set ​[3996] added 2010-11-18 12:55:17 by olle should read:

(In ​[3996]) Refs #707. Refs #534. Class/file gui/form/MascotParameterSetStoragePropertiesForm.java in client/servlet/ updated:

1.Public constructor MascotParameterSetStoragePropertiesForm() updated by change of table field set title key string to "MascotParameterSetStorageProperties", which is more appropriate.

[olle]

(In [3997]) Refs #707. Refs #471. First version of support for editing of OMSSA parameter set storage properties:

1. New class/file action/omssa/ViewOMSSAParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing OMSSAParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VOMSSAPARAMETERSETSTORAGEID in new class ViewActiveOMSSAParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/omssa/ViewActiveOMSSAParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VOMSSAPARAMETERSETSTORAGEID, and gets the corresponding OMSSAParameterSetStorage item, whose properties are shown using new form OMSSAParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveOMSSAParameterSetStorageProperties.

3. New class/file gui/form/OMSSAParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of an OMSSAParameterSetStorage item.

4. New class/file action/omssa/SaveOMSSAParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the OMSSAParameterSetStoragePropertiesForm form and saves them in the corresponding OMSSAParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

(In [3998]) Refs #707. Refs #362. Refs #287. First version of support for editing of X!Tandem parameter set storage properties:

1. New class/file action/xTandemInput/ViewXTandemParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing XTandemParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VXTANDEMPARAMETERSETSTORAGEID in new class ViewActiveXTandemParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/xTandemInput/ViewActiveXTandemParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VXTANDEMPARAMETERSETSTORAGEID, and gets the corresponding XTandemParameterSetStorage item, whose properties are shown using new form XTandemParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveXTandemParameterSetStorageProperties.

3. New class/file gui/form/XTandemParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of a XTandemParameterSetStorage item.

4. New class/file action/xTandemInput/SaveXTandemParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the XTandemParameterSetStoragePropertiesForm form and saves them in the corresponding XTandemParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

The ticket is closed, as the desired functionality has been added. Should problems with the current solution appear, this ticket may be reopened, or a new ticket created.